将 Matlab 转换为 Octave 是否有 container.Map 等价物? [英] Converting Matlab to Octave is there a containers.Map equivalent?
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问题描述
我正在尝试将 Maia 包中的一些 matlab 代码转换成可以使用的东西与八度.我目前陷入困境，因为其中一个文件对 containers.Map 进行了多次调用，这显然是具有 尚未在 octave 中实现.有没有人有任何想法可以轻松实现类似的功能，而无需在 octave 中做大量额外的工作?感谢大家的宝贵时间.
I am trying to convert some matlab code from the Maia package into something that will work with Octave. I am currently getting stuck because one of the files has several calls to containers.Map which is apparently something that has not yet been implemented in octave. Does anyone have any ideas for easily achieving similar functionality without doing a whole lot of extra work in octave? Thanks all for your time.
function [adj_direct contig_direct overlap names longest_path_direct...
weigth_direct deltafiles deltafiles_ref ReferenceAlignment ...
contig_ref overlap_ref name_hash_ref] = ...
assembly_driver(assemblies,ref_genome,target_chromosome, ...
deltafiles_ref,contig_ref, overlap_ref, ...
name_hash_ref, varargin)
% ASSEMBLY_DRIVER Combines contig sets into one assembled chromosome
%
% INPUT
% assemblies
% ref_chromosome
% Startnode_name
% Endnode_name
% OPTIONAL DEFAULT
% 'z_weigths' [.25 .25 .25 .25]
% 'clipping_thrs' 10
% 'ref_distance' -10
% 'ref_quality' 1E-5
% 'max_chromosome_dist' 100
% 'quit_treshold' 15
% 'tabu_time' 3
% 'minimum_improvement' -inf
% 'ref_node_assemblies' all assemblies (slow)
% 'endextend' true
%
%
% SET DEFAULTS
% General parameters
z_weights = [.25 .25 .25 .25];
clipping_thrs = 10;
mapfilter = '-rq';
alignlen = 75;
ident = 85;
% Reference nod parameters
ref_distance = -10;
ref_quality = 1E-5;
max_chromosome_dist = 100;
% TABU parameters
quit_treshold = 15;
tabu_time = 3;
minimum_improvement = -inf;
ref_node_assemblies = assemblies;
% Extending the assembly outwards from the start and en node
endextend = true;
AllowReverse = true;
% If no start and end node are given, they will be determined from tiling
Startnode_name = '';
Endnode_name = '';
containment_edge = true;
ref_first = true;
% If contigs have already been aligned to the reference, give the
% deltafile
ReferenceAlignment = 'NotYetDoneByMaia';
% Get VARARGIN user input
if length(varargin) > 0
while 1
switch varargin{1}
case 'Startnode_name'
Startnode_name = varargin{2};
case 'Endnode_name'
Endnode_name = varargin{2};
case 'z_weigths'
z_weights = varargin{2};
case 'clipping_thrs'
clipping_thrs = varargin{2};
case 'ref_distance'
ref_distance = varargin{2};
case 'ref_quality'
ref_quality = varargin{2};
case 'max_chromosome_dist'
max_chromosome_dist = varargin{2};
case 'quit_treshold'
quit_treshold = varargin{2};
case 'tabu_time'
tabu_time = varargin{2};
case 'minimum_improvement'
minimum_improvement = varargin{2};
case 'ref_node_assemblies'
ref_node_assemblies = assemblies(varargin{2},:);
case 'extend_ends'
endextend = assemblies(varargin{2},:);
case 'AllowReverse'
AllowReverse = varargin{2};
case 'ReferenceAlignment'
ReferenceAlignment = varargin{2};
case 'containment_edge'
containment_edge = varargin{2};
case 'ref_first'
ref_first = varargin{2};
case 'mapfilter'
mapfilter = varargin{2};
case 'alignlen'
alignlen = varargin{2};
case 'ident'
ident = varargin{2};
otherwise
error(['Input ' varargin{2} ' is not known']);
end
if length(varargin) > 2
varargin = varargin(3:end);
else
break;
end
end
end
% Read input assemblies
assembly_names = assemblies(:,1);
assembly_locs = assemblies(:,2);
assembly_quality = containers.Map(assemblies(:,1),assemblies(:,3));
assembly_quality('reference') = ref_quality;
% Read input assemblies for creation of reference nodes
ref_node_assembly_names = ref_node_assemblies(:,1);
ref_node_assembly_locs = ref_node_assemblies(:,2);
ref_node_assembly_quality = containers.Map(ref_node_assemblies(:,1),ref_node_assemblies(:,3));
ref_node_assembly_quality('reference') = ref_quality;
% If there is only one assembly there is nothing to align
if size(assemblies,1) >= 2
% Align assemblies against each other
assembly_pairs = {};
coordsfiles = [];
deltafiles = [];
for i = 1:length(assembly_locs)-1
for j = i+1:length(assembly_locs)
[coordsfile,deltafile] = align_assemblies({assembly_locs{i},assembly_locs{j}},{assembly_names{i}, assembly_names{j}}, ...
mapfilter, alignlen, ident);
coordsfiles = [coordsfiles; coordsfile];
%deltafiles = [deltafiles deltafile];
deltafiles = [deltafiles; {deltafile}];
assembly_pairs = [assembly_pairs;[assembly_names(i) assembly_names(j)]];
end
end
% fprintf('Loading alignment files.
');
% load alignments_done;
% Put the nucmer alignments in an adjency matrix
%[adj, names, name_hash, contig, overlap] = get_adj_matrix(coordsfiles, assembly_pairs, assembly_quality, z_weights, 'clipping_thrs', clipping_thrs, 'dove_tail', 'double','edge_weight','z-scores', 'containment_edge', true);
[adj, names, name_hash, contig, overlap] = get_adj_matrix(deltafiles, assembly_pairs, assembly_quality, z_weights, 'clipping_thrs', clipping_thrs, 'dove_tail', 'double','edge_weight','z-scores', 'containment_edge', containment_edge);
% Merge deltafiles
deltafilesnew = deltafiles{1};
if size(deltafiles,1) > 1
for di = 2:size(deltafiles,1)
deltafilesnew = [deltafilesnew deltafiles{di}];
end
end
deltafiles = deltafilesnew;
else
assembly_pairs = {};
coordsfiles = [];
deltafiles = [];
adj = [];
names = {};
name_hash = containers.Map;
contig = struct('name',{},'size',[],'chromosome',[],'number',[], 'assembly', [], 'assembly_quality', []);
overlap = struct('Q',{},'R',[],'S1',[],'E1', [], 'S2', [], 'E2', [], 'LEN1', [], 'LEN2', [], 'IDY', [], 'COVR', [], 'COVQ', [],'LENR',[], 'LENQ',[]);
end
% Ad the pseudo nodes to the graph. If the contigs have already been
% aligned to the reference genome, just select the alignments that
% correspond to the target chromosome
if isequal(ReferenceAlignment,'NotYetDoneByMaia')
% Align all contigs in 'contig_sets_fasta' to the reference chromosome
[contig_ref, overlap_ref, name_hash_ref, deltafiles_ref] = align_contigs_sets(...
ref_genome, ref_node_assembly_locs, ref_node_assembly_names, ...
ref_node_assembly_quality, clipping_thrs, z_weights, ...
ref_distance,max_chromosome_dist);
ReferenceAlignment = 'out2.delta';
end
% Select only the entries in the deltafile for the current target chromosome
[contig_target_ref, overlap_target_ref, name_hash_target_ref, delta_target_ref] = ...
GetVariablesForTargetChromosome(...
contig_ref, overlap_ref, deltafiles_ref);
% Ref clipping should be high in case of tiling
%if isequal(max_chromosome_dist,'tiling')
% clipping_thrs = 10000
%end
% Add reference nodes to the adjency matrix
[adj, names, name_hash, contig, overlap, delta_target_ref, Startnode_name, Endnode_name] = get_reference_nodes( ...
adj, names, name_hash, contig, overlap, target_chromosome, ...
contig_target_ref, overlap_target_ref, name_hash_target_ref, delta_target_ref, ...
max_chromosome_dist, ref_distance, clipping_thrs, ref_first,...
Startnode_name, Endnode_name, AllowReverse);
% Give reference edges some small extra value to distict between
% assemblies to which a reference node leads
% adj = rank_reference_edges(adj,contig,assembly_quality);
% Specify a start and an end node for the assembly
Startnode = name_hash(Startnode_name);
Endnode = name_hash(Endnode_name);
% Find the best scoring path
fprintf('Directing the final graph
');
% Calculate path on undirected graph to get an idea on how to direct the graph
[longest_path weigth] = longest_path_tabu(adj, Startnode, Endnode, quit_treshold, tabu_time, minimum_improvement);
% Make the graph directed (greedy)
[adj_direct contig_direct] = direct_graph(adj,overlap, contig, names, name_hash,clipping_thrs, Startnode, longest_path, true, ref_first);
% Calcultate final layout-path
fprintf('Find highest scoring path
');
[longest_path_direct weigth_direct] = longest_path_tabu(adj_direct, Startnode, Endnode, quit_treshold, tabu_time, minimum_improvement);
function [contig_target_ref, overlap_target_ref, name_hash_target_ref, delta_target_ref] = ...
GetVariablesForTargetChromosome(...
contig_ref, overlap_ref, deltafiles_ref)
% Select only the entries in the deltafile for the current target chromosome
delta_target_ref = deltafiles_ref;
for di = size(delta_target_ref,2):-1:1
if ~isequal(delta_target_ref(di).R,target_chromosome)
delta_target_ref(di) = [];
end
end
overlap_target_ref = overlap_ref;
for oi = size(overlap_target_ref,2):-1:1
if ~isequal(overlap_target_ref(oi).R,target_chromosome)
overlap_target_ref(oi) = [];
end
end
contig_target_ref = contig_ref;
for ci = size(contig_target_ref,1):-1:1
if isequal(contig_target_ref(ci).assembly, 'reference') && ~isequal(contig_target_ref(ci).name,target_chromosome)
contig_target_ref(ci) = [];
end
end
name_hash_target_ref = make_hash({contig_target_ref.name}');
end
end
推荐答案
据我所知，Octave 中没有与 containers.Map 完全等价的东西...
There is no exact equivalent of containers.Map in Octave that I know of...
一种选择是使用 java 包来创建 java.util.Hashtable.使用这个示例:
One option is to use the java package to create java.util.Hashtable. Using this example:
pkg load java
d = javaObject("java.util.Hashtable");
d.put('a',1)
d.put('b',2)
d.put('c',3)
d.get('b')
<小时>
如果您愿意进行一些重写，您可以使用内置的 struct 作为基本哈希表，其中字符串(有效的变量名)作为键，几乎所有内容都存储在值中.
If you are willing to do a bit of rewriting, you can use the builtin struct as a rudimentary hash table with strings (valid variable names) as keys, and pretty much anything stored in values.
例如，给定以下内容:
keys = {'Mon','Tue','Wed'}
values = {10, 20, 30}
你可以替换这个:
map = containers.Map(keys,values);
map('Mon')
作者:
s = struct();
for i=1:numel(keys)
s.(keys{i}) = values{i};
end
s.('Mon')
您可能需要使用 genvarname 来生成有效的密钥，或者可能需要使用适当的散列函数来生成有效的密钥字符串.
You might need to use genvarname to produce valid keys, or maybe a proper hashing function that produces valid key strings.
还要研究结构相关的函数:getfield、setfield、isfield、fieldnames、rmfield 等.
Also look into struct-related functions: getfield, setfield, isfield, fieldnames, rmfield, etc..
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